Pleurotus eryngii (DC:Fr.) Quel. is a cultivated mushroom of high culinary value and medicinal properties. Mycelium of P. eryngii is characterized by the ability of effective bio-elements absorption from growth media so it could be biofortified with trace elements with a functional activity in the human body. In this study, the ability of P. eryngii mycelia from in vitro cultures as well as fruiting bodies were investigated in terms of their effectiveness in zinc and selenium accumulation. The effect of Se and Zn biofortification on productivity, chemical compounds, and bio-elements content of P. eryngii was determined as well. To enhance Se and Zn content in P. eryngii fruiting bodies and mycelia, substrates were supplemented with sodium selenite, at a concentration of 50 mg L−1, zinc sulfate, and zinc hydro-aspartate at a concentration of 87.2 and 100.0 mg L−1, respectively. Mentioned Zn concentrations contained the same amount of zinc(II) ions, namely 20 mg L−1. The content of organic compounds include phenolic compounds and lovastatin, which were determined by a high-performance liquid chromatography with diode-array detector (HPLC-DAD) and reverse phase high-performance liquid chromatography (RP-HPLC) method with UV detection. The ability of P. eryngii to accumulate zinc and selenium from the culture medium was demonstrated. The degree of accumulation of zinc turned out to be different depending on the type of salt used. The present study also showed that conducting mycelium of P. eryngii in in vitro culture, with a higher content of zinc ions, can result in obtaining the materials with better antioxidant ability. The results of this study can be used to develop the composition of growing media, which ensures the production of biomass with the desired composition of elements.